Neobacillus
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB35415 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K).
2011-01-17 | GSE24361 | GEO
Project description:Bacteria belonging to phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils. To date, only two Gemmatimonadetes strains have been characterized. Here we report the complete genome sequence and methylation pattern of Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411), the first characterized Gemmatimondetes strain isolated from soil.
2014-03-12 | GSE55390 | GEO
Project description:Bacteria belonging to phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils. To date, only two Gemmatimonadetes strains have been characterized. Here we report the complete genome sequence and methylation pattern of Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411), the first characterized Gemmatimondetes strain isolated from soil. Examination of the methylome of Gemmatirosa kalamazoonenis KBS708 using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS
2014-03-12 | E-GEOD-55390 | biostudies-arrayexpress
Project description:M. oryzae 70-15 was treated with multiple bacteria which inhibit 70-15's growth. The bacterial treatments were EA105, a pseudomonad naturally isolated from rice soil, as well as P. fluorescens biocontrol strain CHAO and the cyanide non-producing mutant of CHAO, CHA77.
2014-06-30 | GSE49597 | GEO
Project description:The oxalate-carbonate Pathway (OCP) refers to the biotransformation process of soil Oxalate degradation and coupled Carbonate formation. It is of great significance to explore this complex biotransformation process to improve the suitable rhizosphere environment and promote soil carbon cycle. A strain of oxalate degrading bacteria, Spirillum OX-1, was isolated from soil.
2023-04-17 | PXD041599 |
Project description:We present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and couple this to in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The proteins were extracted from the soil and analysed via LC-MS/MS measurements.
2018-01-08 | PXD007817 | Pride
Project description:Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K). Acetobacter aceti NBRC14818 was cultivated in the medium containing ethanol, acetate, glucose, or mix of ethanol and glucose as carbon sources in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3-0.4. The experiment was performed in duplicate independent cultures.
2011-01-17 | E-GEOD-24361 | biostudies-arrayexpress
Project description:Indole-3-acetic acid (IAA), knows as common plant hormone, is one of the most distributed indole derivatives in the environment. A novel strain, which was able to use IAA as sole source of carbon and nitrogen, was isolated from farm soil, identified and classified as Pseudomonas composti LY1 based on 16S rRNA sequence and genome analysis. The optimal growth conditions for LY1 with IAA are characterized. Proteome profile of strain LY1 to IAA and citrate were analyzed and compared using label free strategy with LC-MS/MS.
2021-09-08 | PXD014968 | Pride
Project description:Data from multiple high throughput technologies such as RNA sequencing (RNA-Seq) and protein mass spectrometry (MS/MS) are often used to assist in predicting eukaryote genome features such as genes, splice variants, and single nucleotide variants (SNVs). The genomes of parasitic nematodes causing neglected tropical diseases are often poorly annotated. Angiostrongylus costaricensis, a nematode that causes an intestinal inflammatory disease known as abdominal angiostrongyliasis (AA), is one example. Currently, no drugs or treatments are available for AA, a public health problem in Latin America, especially in Costa Rica and Brazil. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction supplemented the reference annotation with a) novel coding and non-coding genes; b) pieces of evidence of alternative splicing generating new proteoforms; c) a list of SNVs specific to the Brazilian strain (Crissiumal). To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of a parasitic nematode. We hope this supplemented genome annotation can assist the future development of drugs to treat AA caused by either Brazil strain (Crissiumal) or Costa Rica strain.
2023-03-11 | PXD034605 | Pride